Your message dated Wed, 30 Mar 2022 12:03:57 +0000
with message-id <e1nzx3n-000cgj...@fasolo.debian.org>
and subject line Bug#1008380: fixed in macromoleculebuilder 3.5+dfsg-5
has caused the Debian Bug report #1008380,
regarding macromoleculebuilder: FTBFS: DensityMap.cpp:476:64: error:
‘gemmi::GridSetup’ has not been declared
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
1008380: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1008380
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: macromoleculebuilder
Version: 3.5+dfsg-4
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20220326 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> /usr/bin/c++ -DBuildNtC -DLEPTON_BUILDING_STATIC_LIBRARY -DLepton_USAGE
> -DMMBlib_EXPORTS -DUSE_MMB_CONSTEXPR -DUSE_OPENMM -isystem
> /<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem
> /usr/include/openmm -isystem /usr/include/openmm/reference -isystem /include
> -isystem /<<PKGBUILDDIR>>/3rdparty/Lepton1.3/include -D BuildNtC -D
> USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -O0
> -fvisibility=hidden -O3 -DNDEBUG -fPIC -DMMB_BUILDING_SHARED_LIBRARY
> -std=c++14 -MD -MT CMakeFiles/MMBlib.dir/src/CifOutput.cpp.o -MF
> CMakeFiles/MMBlib.dir/src/CifOutput.cpp.o.d -o
> CMakeFiles/MMBlib.dir/src/CifOutput.cpp.o -c
> /<<PKGBUILDDIR>>/src/CifOutput.cpp
> In file included from /usr/include/gemmi/to_mmcif.hpp:80,
> from /<<PKGBUILDDIR>>/src/CifOutput.cpp:10:
> /usr/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system
> stb_sprintf.h, not the bundled one. It may not work." [-Wcpp]
> 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may
> not work."
> | ^~~~~~~
> /<<PKGBUILDDIR>>/src/DensityMap.cpp: In member function ‘void
> DensityMap::loadParametersAndDensity_CCP4MAP()’:
> /<<PKGBUILDDIR>>/src/DensityMap.cpp:476:64: error: ‘gemmi::GridSetup’ has not
> been declared
> 476 | map.setup (
> gemmi::GridSetup::ReorderOnly, NAN );
> |
> ^~~~~~~~~
> [ 68%] Building CXX object CMakeFiles/MMBlib.dir/src/ProgressWriter.cpp.o
> /usr/bin/c++ -DBuildNtC -DLEPTON_BUILDING_STATIC_LIBRARY -DLepton_USAGE
> -DMMBlib_EXPORTS -DUSE_MMB_CONSTEXPR -DUSE_OPENMM -isystem
> /<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem
> /usr/include/openmm -isystem /usr/include/openmm/reference -isystem /include
> -isystem /<<PKGBUILDDIR>>/3rdparty/Lepton1.3/include -D BuildNtC -D
> USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -O0
> -fvisibility=hidden -O3 -DNDEBUG -fPIC -DMMB_BUILDING_SHARED_LIBRARY
> -std=c++14 -MD -MT CMakeFiles/MMBlib.dir/src/ProgressWriter.cpp.o -MF
> CMakeFiles/MMBlib.dir/src/ProgressWriter.cpp.o.d -o
> CMakeFiles/MMBlib.dir/src/ProgressWriter.cpp.o -c
> /<<PKGBUILDDIR>>/src/ProgressWriter.cpp
> [ 71%] Building CXX object
> CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o
> /usr/bin/c++ -DBuildNtC -DLEPTON_BUILDING_STATIC_LIBRARY -DLepton_USAGE
> -DMMBlib_EXPORTS -DUSE_MMB_CONSTEXPR -DUSE_OPENMM -isystem
> /<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem
> /usr/include/openmm -isystem /usr/include/openmm/reference -isystem /include
> -isystem /<<PKGBUILDDIR>>/3rdparty/Lepton1.3/include -D BuildNtC -D
> USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -O0
> -fvisibility=hidden -O3 -DNDEBUG -fPIC -DMMB_BUILDING_SHARED_LIBRARY
> -std=c++14 -MD -MT CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o -MF
> CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o.d -o
> CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o -c
> /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp
> make[3]: *** [CMakeFiles/MMBlib.dir/build.make:345:
> CMakeFiles/MMBlib.dir/src/DensityMap.cpp.o] Error 1
The full build log is available from:
http://qa-logs.debian.net/2022/03/26/macromoleculebuilder_3.5+dfsg-4_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
--- Begin Message ---
Source: macromoleculebuilder
Source-Version: 3.5+dfsg-5
Done: Andrius Merkys <mer...@debian.org>
We believe that the bug you reported is fixed in the latest version of
macromoleculebuilder, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1008...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <mer...@debian.org> (supplier of updated macromoleculebuilder
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 30 Mar 2022 06:37:26 -0400
Source: macromoleculebuilder
Architecture: source
Version: 3.5+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Andrius Merkys <mer...@debian.org>
Closes: 1008380
Changes:
macromoleculebuilder (3.5+dfsg-5) unstable; urgency=medium
.
* Fix compatibility with Gemmi >= 0.5.3 (Closes: #1008380).
* Bump copyright years.
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